Generic OBO source?

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Generic OBO source?

Sam Hokin-3
Is there a way to employ a generic OBO source rather than creating specific ones for each ontology? I've got lots of ontologies with
many more to come:

cowpea-crop-ontology
plant-ontology
plant-trait-ontology
soybean-crop-ontology
soybean-ontology

I'd like to simply use a source called "obo" or something and put the relevant data into project.xml rather than in
blah-ontology/blah-ontology.properties.

I presume I'd need to hack plugin/src/main/groovy/org/intermine/plugin/integrate/IntegrateUtils.groovy but I'm down with that. But I
thought I'd ask in case there's already a way to do it.

It seems silly to create a new source which simply has different properties, no code.
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Re: Generic OBO source?

Paulo Nuin
Hi Sam

I have been doing this for a while with anatomy, disease and another OBO file. I just extended the default OBO loader and create specific loaders for these classes using the Intermine new source script.

One thing that might happen is a collision of elements if you have similar items coming from another source type with similar information. But, you know more than me on how to avoid that and merge them.

Cheers

Paulo


> On Jun 24, 2020, at 9:58 AM, Sam Hokin <[hidden email]> wrote:
>
> Is there a way to employ a generic OBO source rather than creating specific ones for each ontology? I've got lots of ontologies with many more to come:
>
> cowpea-crop-ontology
> plant-ontology
> plant-trait-ontology
> soybean-crop-ontology
> soybean-ontology
>
> I'd like to simply use a source called "obo" or something and put the relevant data into project.xml rather than in blah-ontology/blah-ontology.properties.
>
> I presume I'd need to hack plugin/src/main/groovy/org/intermine/plugin/integrate/IntegrateUtils.groovy but I'm down with that. But I thought I'd ask in case there's already a way to do it.
>
> It seems silly to create a new source which simply has different properties, no code.
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Generic OBO source?

Sam Hokin-3
In reply to this post by Sam Hokin-3
Thanks, Paulo. I've got no problem creating new loaders -- I'd like a _single_ obo loader which is instructed to load a particular
OBO file in project.xml. The only difference between OBO loaders is the properties file. It's pretty easy to create a generic "obo"
loader and tweak IntegrateUtils.groovy to read the properties from project.xml, as the gff loader does, but I thought I'd check here
first.

BTW, I only use OntologyTerm as a class; every ontology identifier has a unique prefix (GO:, SOY:, CO_336:, etc.) I got rid of
GOTerm as well in my mines, they're just OntologyTerms with the GO: prefix. There's nothing really special about the Gene Ontology.
The Sequence Ontology is a bit special, given how it's associated with classes in InterMine.

On 6/24/20 10:02 AM, Paulo Nuin wrote:

> Hi Sam
>
> I have been doing this for a while with anatomy, disease and another OBO file. I just extended the default OBO loader and create specific loaders for these classes using the Intermine new source script.
>
> One thing that might happen is a collision of elements if you have similar items coming from another source type with similar information. But, you know more than me on how to avoid that and merge them.
>
> Cheers
>
> Paulo
>
>
>> On Jun 24, 2020, at 9:58 AM, Sam Hokin <[hidden email]> wrote:
>>
>> Is there a way to employ a generic OBO source rather than creating specific ones for each ontology? I've got lots of ontologies with many more to come:
>>
>> cowpea-crop-ontology
>> plant-ontology
>> plant-trait-ontology
>> soybean-crop-ontology
>> soybean-ontology
>>
>> I'd like to simply use a source called "obo" or something and put the relevant data into project.xml rather than in blah-ontology/blah-ontology.properties.
>>
>> I presume I'd need to hack plugin/src/main/groovy/org/intermine/plugin/integrate/IntegrateUtils.groovy but I'm down with that. But I thought I'd ask in case there's already a way to do it.
>>
>> It seems silly to create a new source which simply has different properties, no code.
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Generic OBO source?

Daniela Butano-2
Hi Sam,
at the moment there is not a generic-obo converter.
It might be nice/useful to have it and add to the intermine/bio-sources.
At the moment you can pass (for sure, I jave just tested few days ago)
<property name="dataset" value="My Sequence Ontology Data Set"/>
<property name="datasource" value="My Sequence Ontology Data Source"/>
to create a data set/source with a different label than the
obo.ontology.name

Daniela


> Thanks, Paulo. I've got no problem creating new loaders -- I'd like a
> _single_ obo loader which is instructed to load a particular OBO file
> in project.xml. The only difference between OBO loaders is the
> properties file. It's pretty easy to create a generic "obo" loader and
> tweak IntegrateUtils.groovy to read the properties from project.xml,
> as the gff loader does, but I thought I'd check here first.
>
> BTW, I only use OntologyTerm as a class; every ontology identifier has
> a unique prefix (GO:, SOY:, CO_336:, etc.) I got rid of GOTerm as well
> in my mines, they're just OntologyTerms with the GO: prefix. There's
> nothing really special about the Gene Ontology. The Sequence Ontology
> is a bit special, given how it's associated with classes in InterMine.
>
> On 6/24/20 10:02 AM, Paulo Nuin wrote:
>> Hi Sam
>>
>> I have been doing this for a while with anatomy, disease and another
>> OBO file. I just extended the default OBO loader and create specific
>> loaders for these classes using the Intermine new source script.
>>
>> One thing that might happen is a collision of elements if you have
>> similar items coming from another source type with similar
>> information. But, you know more than me on how to avoid that and merge
>> them.
>>
>> Cheers
>>
>> Paulo
>>
>>
>>> On Jun 24, 2020, at 9:58 AM, Sam Hokin <[hidden email]> wrote:
>>>
>>> Is there a way to employ a generic OBO source rather than creating
>>> specific ones for each ontology? I've got lots of ontologies with
>>> many more to come:
>>>
>>> cowpea-crop-ontology
>>> plant-ontology
>>> plant-trait-ontology
>>> soybean-crop-ontology
>>> soybean-ontology
>>>
>>> I'd like to simply use a source called "obo" or something and put the
>>> relevant data into project.xml rather than in
>>> blah-ontology/blah-ontology.properties.
>>>
>>> I presume I'd need to hack
>>> plugin/src/main/groovy/org/intermine/plugin/integrate/IntegrateUtils.groovy
>>> but I'm down with that. But I thought I'd ask in case there's already
>>> a way to do it.
>>>
>>> It seems silly to create a new source which simply has different
>>> properties, no code.
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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